rs1801260
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004898(CLOCK):c.*213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152032 control chromosomes in the gnomAD Genomes database, including 4955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 4955 hom., cov: 32)
Consequence
CLOCK
NM_004898 3_prime_UTR
NM_004898 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.802
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLOCK | NM_004898.4 | c.*213T>C | 3_prime_UTR_variant | 23/23 | ENST00000513440.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLOCK | ENST00000513440.6 | c.*213T>C | 3_prime_UTR_variant | 23/23 | 1 | NM_004898.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.246 AC: 37470AN: 152032Hom.: 4955 Cov.: 32
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GnomAD4 exome AF: 0.272 AC: 118169AN: 435170Hom.: 16931 AF XY: 0.278 AC XY: 63693AN XY: 229406
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at